6-119193769-T-C
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_005907.4(MAN1A1):c.1326+8A>G variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000522 in 1,590,838 control chromosomes in the GnomAD database, including 6 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_005907.4 splice_region, intron
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
MAN1A1 | NM_005907.4 | c.1326+8A>G | splice_region_variant, intron_variant | Intron 9 of 12 | ENST00000368468.4 | NP_005898.2 | ||
MAN1A1 | XM_005266986.5 | c.1575+8A>G | splice_region_variant, intron_variant | Intron 9 of 12 | XP_005267043.1 | |||
MAN1A1 | XM_011535833.3 | c.759+8A>G | splice_region_variant, intron_variant | Intron 8 of 11 | XP_011534135.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00275 AC: 419AN: 152210Hom.: 4 Cov.: 33
GnomAD3 exomes AF: 0.000770 AC: 189AN: 245486Hom.: 3 AF XY: 0.000566 AC XY: 75AN XY: 132512
GnomAD4 exome AF: 0.000284 AC: 408AN: 1438510Hom.: 2 Cov.: 26 AF XY: 0.000241 AC XY: 173AN XY: 716804
GnomAD4 genome AF: 0.00277 AC: 422AN: 152328Hom.: 4 Cov.: 33 AF XY: 0.00250 AC XY: 186AN XY: 74494
ClinVar
Submissions by phenotype
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at